Northern announced on Saturday morning that all lines at Huddersfield Station were closed - but at 12.30pm it was announced lines were open once more.
The signalling fault impacted the Leeds-Manchester Victoria via Brighouse line, with services being diverted.
TransPennine Express tweeted: "Due to signalling staff being taken ill between #ManchesterPiccadilly and #Leeds all lines are closed. Please avoid travel until later this afternoon."
Customers affected by the disruption were able to use their tickets to travel on other services including Cross Country between Leeds and Edinburgh, East Midlands Railway between Liverpool - Manchester - Sheffield, Grand Central Rail between York and Northallerton, and LNER between Leeds/York - Doncaster and York - Edinburgh.
Tickets were also being accepted on Northern - via any reasonable route - and Manchester Metrolink between Manchester Piccadilly and Manchester Victoria.
Meanwhile, the Huddersfield-Sheffield service was only running between Penistone and Sheffield, and trains from Huddersfield to Bradford Interchange were cancelled.
Further rail disruption hit the line between Beverley and Scarborough on Saturday morning after signalling staff were taken ill - but disruption to this route has now been resolved.